MolNFT v1 · #138754 · protein
L-homocysteine-bound nifs from helicobacter pylori
5WT5 · Cysteine desulfurase iscs: “L-homocysteine-bound nifs from helicobacter pylori”. X-ray diffraction, 1 ligand (HCS), 16 pockets (best druggability 0.78). MolNFT v1 #138754 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WT5
- Type
- protein
- Length
- 1,455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase iscs
- EC
- 2.8.1.7
- UniProt
- O25008
- Ligands
- HCS
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase iscs (EC 2.8.1.7) | protein | 363 | 42% helix, 17% strand | O25008 |
| B | Cysteine desulfurase iscs (EC 2.8.1.7) | protein | 363 | 43% helix, 18% strand | O25008 |
| C | Cysteine desulfurase iscs (EC 2.8.1.7) | protein | 364 | 41% helix, 17% strand | O25008 |
| D | Cysteine desulfurase iscs (EC 2.8.1.7) | protein | 365 | 43% helix, 17% strand | O25008 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · 4 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.78 | 0.91 | 27 | empty |
| 2 | 218 | 0.78 | 0.91 | 26 | empty |
| 3 | 403 | 0.63 | 0.78 | 46 | HCS |
| 4 | 349 | 0.62 | 0.79 | 41 | HCS |
| 5 | 423 | 0.62 | 0.77 | 44 | HCS |
Interfaces
2 interfaces between chains.
- C–D · 2668 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2641 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O25008
- Elsewhere: RCSB PDB 5WT5 · PDBe 5WT5 · UniProt O25008
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